Recount Metadata pre-processing and correlations
Urwah Nawaz
2023-07-10
Setup
Background
Datasets
Ramakar et al (2017)
- Selection of metadata variables for subset
## V1
## RunID -0.92207331
## SampleID 0.56588402
## SampleACC 0.52187022
## ExperimentACC 0.52227248
## ExperimentTitle 0.52227248
## SampleAttributes -0.72217656
## ExperimentAttributes 0.52227248
## SampleName 0.52227248
## SampleTitle -1.23951411
## SampleBases 1.12469750
## SampleSpots 1.12469750
## RunPublished 0.55583963
## Size 1.13646420
## RunTotalBases 1.12469750
## RunTotalSpots 1.12469750
## NumSpots 1.12469750
## ReadInfo 0.39151818
## RunAlias 0.56588402
## ChimericPairs 0.01401913
## Percent_aligned_ChrX -1.10900870
## Percent_aligned_ChrY -1.22596746
## AUC_all_alignments 1.16003963
## AUC_all_annotated_exons 1.15464673
## AUC_uniquely_aligned 1.15450709
## AUC_all_annotated_exons_unique 1.15267282
## AUC_all_percentage -0.20375605
## AUC_unique_percentage -0.32956490
## TotalNFragments 1.15974100
## ReadFragmentLength 1.16334602
## MeanFragmentLength -0.74930177
## MeanFragmentLength_BAM -1.44864053
## ModeFragmentLength -1.36344896
## ModeFragmentLengthCount 0.98793867
## Percentage_fragment_mapped_exon_fc -0.82778239
## Percentage_fragment_mapped_unique_exon_fc -0.92522176
## Total_fragments_input_fc_exon_fc 1.15700790
## Total_fragments_assigned_exon_fc 1.08295864
## Total_fragments_count_unique_exon_fc 1.15700790
## Total_fragments_count_unique_assigned_exon_fc 1.08295864
## Percentage_fragment_mapped_gene_fc -0.75947235
## Percentage_fragment_mapped_unique_gene_fc -0.88428933
## Total_fragments_input_fc_gene_fc 1.15700790
## Total_fragments_assigned_gene_fc 1.09171621
## Total_fragments_count_unique_gene_fc 1.15700790
## Total_fragments_count_unique_assigned_gene_fc 1.08145691
## IntronTotal 0.71789243
## IntronicRate -0.89706236
## Percentage_chimeric_reads_STAR -0.59599104
## Percentage_mapped_multi_loci_STAR -1.08002420
## Percentage_mapped_too_many_loci_STAR -0.82344064
## Percentage_unmapped_other_STAR -0.57569697
## Percentage_unmapped_too_short_STAR -1.87378200
## ReadsMapped 1.15974100
## Average_mapped_length_STAR -0.31376005
## Deletion_average_length_STAR -0.54905080
## Deteltion_rate_per_base_STAR -0.29299586
## Insertion_average_length_STAR -0.54415312
## Insertion_rate_per_base_STAR -1.51015141
## Mapping_speed_per_hour_STAR -0.95678448
## Percentage_mismatch_per_base_STAR -1.73177086
## Number_of_chimeric_reads_STAR 1.10762237
## TotalNReads 1.12469750
## Number_reads_mapped_to_multiple_loci_STAR 0.95868089
## Number_reads_mapped_to_too_many_loci_STAR 0.81135118
## Number_reads_unmapped_other_STAR 0.52753358
## Number_reads_unmapped_too_short_STAR -0.52434834
## Number_canonical_splices_AT_AC_STAR 0.74891267
## Number_canonical_splices_GC_AG_STAR 0.77264527
## Number_canonical_splices_GT_AG_STAR 0.77206646
## Number_non_canonical_splices_STAR 1.03569281
## Number_splices_total_STAR 0.77455521
## MappingRate -0.25005180
## MappingRate_unique 1.15417303
## Junction_count 0.70888310
## Junction_coverage 0.78152832
## Junction_average_coverage 0.69608728
## Number_input_reads_both_STAR 1.12469750
## All_mapped_reads_both_STAR 1.15974100
## Number_chimeric_reads_both_STAR 1.10762237
## Number_reads_mapped_multiple_loci_both_STAR 0.95868089
## Numner_reads_mapped_too_many_loci_both_STAR 0.81135118
## Number_reads_unmapped_other_both_STAR 0.52753358
## Number_reads_unmapped_too_short_both_STAR -0.52434834
## Number_reads_mapped_uniquely_both_STAR 1.15417303
## MappingRate_both -0.30067430
## Percent_Chimeric_both -0.59525170
## Percentage_mapped_multi_loci_both_STAR -1.07919545
## Percentage_mapped_too_many_loci_both_STAR -0.77900075
## Percentage_unmapped_other_both_STAR -0.71156482
## Percentage_unmapped_too_short_both_STAR -1.87393185
## Percentage_uniquely_mapped_both_STAR -0.24988415
## DIstinctQualityValues -0.38163684
## Percent_Bases 1.12469750
## Percent_A 0.32372534
## Percent_C -2.26309208
## Percent_G -2.29141772
## Percent_T 0.16873923
## Percent_N -1.64022797
## Average_Phred -0.33017200
## ErrQ -0.50054673
## SampleAccPrediction 0.52187022
## PredictionType -1.85518724
## BigWigFile -1.23564405
## Age -0.73338606
## pH -0.98860509
## StructureAcronym -1.05218257
## Diagnosis -1.02821128
## Ethnicity -0.70033387
## Sex -1.28230304
## PMI -1.02004084
## Regions -1.07465807
## Age_rounded -0.73338606
## AgeInterval -0.74480077- Selection for variance Partition
| OriginalMetadataColumnName | BITColumnName | Type |
|---|---|---|
| external_id | SampleID | Sample charactertics |
| sra.run_total_spots | RunTotalSpots | Sequencing metrics |
| recount_qc.aligned_reads..chrm | ChimericPairs | Sequencing metrics |
| recount_qc.aligned_reads..chrx | Percent_aligned_ChrX | Sequencing metrics |
| recount_qc.aligned_reads..chry | Percent_aligned_ChrY | Sequencing metrics |
| recount_qc.bc_auc.all_reads_all_bases | AUC_all_alignments | Sequencing metrics |
| recount_qc.bc_auc.unique_reads_all_bases | AUC_uniquely_aligned | Sequencing metrics |
| recount_qc.bc_auc.all_. | AUC_all_percentage | Sequencing metrics |
| recount_qc.bc_auc.unique_. | AUC_unique_percentage | Sequencing metrics |
| recount_qc.bc_frag.count | TotalNFragments | Sequencing metrics |
| recount_qc.bc_frag.mode_length_count | ModeFragmentLengthCount | Sequencing metrics |
| recount_qc.exon_fc.all_. | Percentage_fragment_mapped_exon_fc | Sequencing metrics |
| recount_qc.exon_fc.unique_. | Percentage_fragment_mapped_unique_exon_fc | Sequencing metrics |
| recount_qc.exon_fc_count_all.total | Total_fragments_input_fc_exon_fc | Sequencing metrics |
| recount_qc.exon_fc_count_all.assigned | Total_fragments_assigned_exon_fc | Sequencing metrics |
| recount_qc.exon_fc_count_unique.total | Total_fragments_count_unique_exon_fc | Sequencing metrics |
| recount_qc.exon_fc_count_unique.assigned | Total_fragments_count_unique_assigned_exon_fc | Sequencing metrics |
| recount_qc.gene_fc.all_. | Percentage_fragment_mapped_gene_fc | Sequencing metrics |
| recount_qc.gene_fc.unique_. | Percentage_fragment_mapped_unique_gene_fc | Sequencing metrics |
| recount_qc.gene_fc_count_all.total | Total_fragments_input_fc_gene_fc | Sequencing metrics |
| recount_qc.gene_fc_count_all.assigned | Total_fragments_assigned_gene_fc | Sequencing metrics |
| recount_qc.gene_fc_count_unique.total | Total_fragments_count_unique_gene_fc | Sequencing metrics |
| recount_qc.gene_fc_count_unique.assigned | Total_fragments_count_unique_assigned_gene_fc | Sequencing metrics |
| recount_qc.intron_sum | IntronTotal | Sequencing metrics |
| recount_qc.intron_sum_. | IntronicRate | Sequencing metrics |
| recount_qc.star.._of_reads_mapped_to_multiple_loci | Percentage_mapped_multi_loci_STAR | Sequencing metrics |
| recount_qc.star.._of_reads_mapped_to_too_many_loci | Percentage_mapped_too_many_loci_STAR | Sequencing metrics |
| recount_qc.star.._of_reads_unmapped._other | Percentage_unmapped_other_STAR | Sequencing metrics |
| recount_qc.star.._of_reads_unmapped._too_many_mismatches | Percentage_unmapped_too_many_mismatches_STAR | Sequencing metrics |
| recount_qc.star.._of_reads_unmapped._too_short | Percentage_unmapped_too_short_STAR | Sequencing metrics |
| recount_qc.star.all_mapped_reads | ReadsMapped | Sequencing metrics |
| recount_qc.star.number_of_input_reads | TotalNReads | Sequencing metrics |
| recount_qc.star.uniquely_mapped_reads_. | MappingRate | Sequencing metrics |
| recount_qc.star.uniquely_mapped_reads_number | MappingRate_unique | Sequencing metrics |
| recount_qc.junction_count | Junction_count | Sequencing metrics |
| recount_qc.junction_coverage | Junction_coverage | Sequencing metrics |
| recount_qc.junction_avg_coverage | Junction_average_coverage | Sequencing metrics |
| recount_qc.star.number_of_input_reads_both | Number_input_reads_both_STAR | Sequencing metrics |
| recount_qc.star.all_mapped_reads_both | All_mapped_reads_both_STAR | Sequencing metrics |
| recount_qc.star.._mapped_reads_both | MappingRate_both | Sequencing metrics |
| recount_qc.star.._reads_mapped_to_multiple_loci_both | Percentage_mapped_multi_loci_both_STAR | Sequencing metrics |
| recount_qc.star.._reads_mapped_to_too_many_loci_both | Percentage_mapped_too_many_loci_both_STAR | Sequencing metrics |
| recount_qc.star.._reads_unmapped._other_both | Percentage_unmapped_other_both_STAR | Sequencing metrics |
| recount_qc.star.._reads_unmapped._too_many_mismatches_both | Percentage_unmapped_too_many_mismatches_both_STAR | Sequencing metrics |
| recount_qc.star.._reads_unmapped._too_short_both | Percentage_unmapped_too_short_both_STAR | Sequencing metrics |
| recount_qc.star.uniquely_mapped_reads_._both | Percentage_uniquely_mapped_both_STAR | Sequencing metrics |
| NA | Age | Phenotype |
| NA | pH | Sequencing metrics |
| NA | StructureAcronym | Sample charactertics |
| NA | Diagnosis | Phenotype |
| NA | Ethnicity | Phenotype |
| NA | Sex | Phenotype |
| NA | PMI | Sequencing metrics |
| NA | Regions | Sample charactertics |
| NA | Period | Phenotype |
| NA | AgeInterval | Phenotype |
